U.S. Interior Secretary Ken Salazar rejected a request Thursday to extend the lease of a controversial oyster farm on the Point Reyes National Seashore, ending more than 100 years of shellfish production in the area and creating the first federal marine wilderness area in California.

Drake's Bay Oyster Co. — which produces 40 percent of the state's oysters — has 90 days to remove all trace of its operations and depart from the bay where Sir Francis Drake first set foot in California.

"The estero is one of our nation's crown jewels, and today we are fulfilling the vision to protect this special place for generations to come," Salazar said in a statement.

The decision comes one week after Salazar visited the oyster farm to meet with owner Kevin Lunny and environmentalists fighting to shutter the operation.

Lunny, who bought the farm in 2004 anticipating the permit would be renewed, said Salazar informed him of the decision by phone. He hung up and walked out of his office, where he shared the news with his 30 anxious employees.

"We've never stood on the docks in tears before," Lunny said. "It's a horrible blow."

Salazar, who had sole authority to extend the farm's 40-year lease or terminate it, ordered the National Park Service to allow the permit to expire so that the bay can return to its natural state.

However, he also directed the Park Service to extend the leases of 15 beef and dairy ranches operating along the Point Reyes seashore. The ranches have "a long and important history on the Point Reyes peninsula," Salazar said.

Wilderness advocates hailed the decision as a victory for the public. A study commissioned by the Park Service warned the oyster farm caused harm to harbor seals and grasses. They urged Salazar to return it to a state of wilderness as designated by Congress in 1976.

"This has been a long time coming," said Bruce Hamilton, deputy executive director of the Sierra Club in San Francisco. "We have been waiting for 40 years. It's the right decision."

Neal Desai, associate director of the National Parks Conservation Association, called it a major conservation achievement.

"This is the greatest gift an Interior Secretary can give us," said Desai. "It's the protection of our national parks and wildlife. Salazar has delivered."

Salazar also was applauded by many Democratic lawmakers, including Sen. Barbara Boxer and Rep. Lynn Woolsey.

"He studied the issue carefully, he listened closely to all sides and, in the end, he made his decision based on the science and the law," Boxer said in a written statement.

Woolsey said Salazar was "fair, thorough and knowledgeable."

"Now that this long process has run its course, it is my hope that we can put the contentiousness behind us and move forward as a united community," Woolsey said.

But Salazar was criticized by Sen. Diane Feinstein, who authored the 2009 legislation that gave Salazar sole discretion to renew the permit.

Feinstein, who had urged Salazar to extend the lease for 10 years, said the Park Service's environmental review contained "false and misleading science."

"The Secretary's decision effectively puts this historic California oyster farm out of business," she said. "As a result, the farm will be forced to cease operations and 30 Californians will lose their jobs."

Lunny's business harvests $1.5 million in shellfish a year from the estuary. He said continued demand for oysters will force distributors to look overseas.

"We have just lost an incredibly important piece of the local food system," Lunny said. "It cannot be replaced by flying in food from Asia."

Oyster farming on the 2,500-acre estuary, a five-fingered estuary on the Marin County coast, dates back nearly 100 years.

The Johnson Oyster Co. operated a facility on the site for 60 years before Lunny took over the lease, which had been set to expire today. The Lunny family has operated a nearby cattle ranch for generations.

The National Seashore, established in 1962 by President John F. Kennedy, gets more than 2 million visitors a year. It protects more than 80 miles of California coastline and is home to harbor seals and migratory birds.